eggNOG v7: A major update to its core phylogenomic resource for orthology inference


An international study co-led by the Comparative Genomics and Metagenomics Group of the CBGP presents, in an article published in Nucleic Acids Research, a new version of the phylogenomic database that allows for refining the prediction of orthologous genes, the evolutionary analysis of protein families and functional annotation in eukaryotes, bacteria and archaea.

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A screenshot of the completely revamped new web interface of eggNOG v7. / CBGP



eggNOG v7 is distinguished by replacing clustering methods based on triangulation of best reciprocal hits with a phylogenetic approach focused on functional domains. This methodology addresses the computational limitations and hierarchical inconsistencies observed in previous versions, especially in the handling of multidomain proteins or those with more complex evolutionary histories.

The new database, presented in an article in the journal Nucleic Acids Research, analyzes a total of 59.3 million proteins from 12,535 species, reconstructing the evolutionary history of each through its functional domains. This change in approach has allowed the generation of Orthologous Groups (OGs) that exhibit greater accuracy and functional consistency. According to the researchers, "this new phylogenetic and domain-centric approach allows us to resolve the conceptual challenges of previous versions, such as the handling of complex proteins and inconsistencies between different taxonomic levels."

The new eggNOG v7 database is complemented by a completely redesigned web interface. This platform is optimized to facilitate the visual and interactive exploration of protein evolution, phylogenetic context, and functional annotations.

A completely redesigned eggnog

The completely redesigned version v7 offers more reliable, detailed, and accessible orthology data through a revamped web interface. The fundamental change lies in its methodology. Previous versions relied on triangulation by best reciprocal hits, a system that, while effective, generated high computational demands, hierarchical inconsistencies, and errors when classifying complex proteins. eggNOG v7 adopts a domain-centric phylogenetic approach. The new analysis method separately reconstructs the evolutionary history of each protein's functional domains. "We have completely redesigned the web interface so that scientists from diverse disciplines can visually and interactively explore a protein's evolution, its phylogenetic context, and its functional annotations," the researchers conclude.




Original Paper:

Hernández-Plaza, A., Deng, Z., Robledo-Yagüe, F., Szklarczyk, D., von Mering, C., Bork, P.✉, Huerta-Cepas, J.✉ 2025. eggNOG v7: phylogeny-based orthology predictions and functional annotations. Nucleic Acids Research gkaf1249. DOI: 10.1093/nar/gkaf1249

 
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